Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple compl...

Fungal xylanases has important applications in food, baking, pulp and paper industries in addition to various other industries. Xylanases are produced extensively by both bacterial and fungal sources and has tremendous potential of being active at extremes of temperature and pH. In the present study an effort has been made to explore the codon bias perspective of this potential enzyme using bio...

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine ...

ABST RACT In this study, we analyzed the synonymous codon usage bias in porcine epidemic diarrhea virus genome. The effective number of codons (ENC) and the relative synonymous codon usage (RSCU) values are used to estimate codon usage variation. The plot of ENC values against GC3s and correlation analysis revealed that mutational pressure rather than translational selection is the main factor ...

This data article contains data related to the article "Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions" by Subramanian and Sarkar, Genomics, 2015 (10.1016/j.ygeno.2015.05.009). The data comprises of sequence-based measures that quantify the effect of codon usage across genomes. The dat...

O código genético é degenerado, isto é, o mesmo amino ácido pode ser codificado por vários codons. Apesar de codificarem o mesmo amino ácido, estes codons sinônimos não são utilizados da mesma forma em genomas diferentes, e mesmo em um único genoma o padrão de uso dos codons sinônimos pode variar muito entre os genes, ou ainda ao longo de um único gene. Com a recente introdução de seqüências ge...

Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and the codon usage, use this bias to predict the expression level of genes. Both indices are based on fairly simple assumptions about which genes are most highly expressed, which were known when they we...

Codon-usage bias has been observed in almost all genomes and is thought to result from selection for efficient and accurate translation of highly expressed genes. Codon usage is also implicated in the control of transcription, splicing and RNA structure. Many genes exhibit little codon-usage bias, which is thought to reflect a lack of selection for messenger RNA translation. Alternatively, howe...